/* ---------------------------------------------------------------------
 *
 * Copyright (C) 2014 - 2019 by the deal.II authors
 *
 * This file is part of the deal.II library.
 *
 * The deal.II library is free software; you can use it, redistribute
 * it, and/or modify it under the terms of the GNU Lesser General
 * Public License as published by the Free Software Foundation; either
 * version 2.1 of the License, or (at your option) any later version.
 * The full text of the license can be found in the file LICENSE.md at
 * the top level directory of deal.II.
 *
 * ---------------------------------------------------------------------

 *
 * Authors: Wolfgang Bangerth, Texas A&M University, 2014
 *          Luca Heltai, SISSA, 2014
 *          D. Sarah Stamps, MIT, 2014
 */

// Let us start with the include files we need here. Obviously, we need the
// ones that describe the triangulation (<code>tria.h</code>), and that allow
// us to create and output triangulations (<code>grid_generator.h</code> and
// <code>grid_out.h</code>). Furthermore, we need the header file that
// declares the Manifold and ChartManifold classes that we will need to
// describe the geometry (<code>manifold.h</code>). We will then also need
// the GridTools::transform() function from the last of the following header
// files; the purpose for this function will become discussed at the point
// where we use it.
#include <deal.II/grid/tria.h>
#include <deal.II/grid/grid_generator.h>
#include <deal.II/grid/grid_out.h>
#include <deal.II/grid/manifold.h>
#include <deal.II/grid/grid_tools.h>

// The remainder of the include files relate to reading the topography data.
// As explained in the introduction, we will read it from a file and then use
// the Functions::InterpolatedUniformGridData class that is declared in the
// first of the following header files. Because the data is large, the file we
// read from is stored as gzip compressed data and we make use of some
// BOOST-provided functionality to read directly from gzipped data.
#include <deal.II/base/function_lib.h>

#include <boost/iostreams/filtering_stream.hpp>
#include <boost/iostreams/filter/gzip.hpp>
#include <boost/iostreams/device/file.hpp>

#include <fstream>
#include <iostream>
#include <memory>


// The final part of the top matter is to open a namespace into which to put
// everything, and then to import the dealii namespace into it.
namespace Step53
{
  using namespace dealii;


  // @sect3{Describing topography: AfricaTopography}
  //
  // The first significant part of this program is the class that describes
  // the topography $h(\hat phi,\hat \theta)$ as a function of longitude
  // and latitude. As discussed in the introduction, we will make our life
  // a bit easier here by not writing the class in the most general way
  // possible but by only writing it for the particular purpose we are
  // interested in here: interpolating data obtained from one very specific
  // data file that contains information about a particular area of the
  // world for which we know the extents.
  //
  // The general layout of the class has been discussed already above.
  // Following is its declaration, including three static member functions
  // that we will need in initializing the <code>topography_data</code>
  // member variable.
  class AfricaTopography
  {
  public:
    AfricaTopography();

    double value(const double lon, const double lat) const;

  private:
    const Functions::InterpolatedUniformGridData<2> topography_data;

    static std::vector<double> get_data();
  };


  // Let us move to the implementation of the class. The interesting parts
  // of the class are the constructor and the <code>value()</code> function.
  // The former initializes the Functions::InterpolatedUniformGridData member
  // variable and we will use the constructor that requires us to pass in
  // the end points of the 2-dimensional data set we want to interpolate
  // (which are here given by the intervals $[-6.983333, 11.98333]$,
  // using the trick of switching end points discussed in the introduction,
  // and $[25, 35.983333]$, both given in degrees), the number of intervals
  // into which the data is split (379 in latitude direction and 219 in
  // longitude direction, for a total of $380\times 220$ data points), and
  // a Table object that contains the data. The data then of course has
  // size $380\times 220$ and we initialize it by providing an iterator
  // to the first of the 83,600 elements of a std::vector object returned
  // by the <code>get_data()</code> function below. Note that all of the
  // member functions we call here are static because (i) they do not
  // access any member variables of the class, and (ii) because they are
  // called at a time when the object is not initialized fully anyway.
  AfricaTopography::AfricaTopography()
    : topography_data({{std::make_pair(-6.983333, 11.966667),
                        std::make_pair(25, 35.95)}},
                      {{379, 219}},
                      Table<2, double>(380, 220, get_data().begin()))
  {}


  double AfricaTopography::value(const double lon, const double lat) const
  {
    return topography_data.value(
      Point<2>(-lat * 180 / numbers::PI, lon * 180 / numbers::PI));
  }


  // The only other function of greater interest is the <code>get_data()</code>
  // function. It returns a temporary vector that contains all 83,600 data
  // points describing the altitude and is read from the file
  // <code>topography.txt.gz</code>. Because the file is compressed by gzip,
  // we cannot just read it through an object of type std::ifstream, but
  // there are convenient methods in the BOOST library (see
  // http://www.boost.org) that allows us to read from compressed files
  // without first having to uncompress it on disk. The result is, basically,
  // just another input stream that, for all practical purposes, looks just like
  // the ones we always use.
  //
  // When reading the data, we read the three columns but throw ignore the
  // first two. The datum in the last column is appended to an array that we
  // the return and that will be copied into the table from which
  // <code>topography_data</code> is initialized. Since the BOOST.iostreams
  // library does not provide a very useful exception when the input file
  // does not exist, is not readable, or does not contain the correct
  // number of data lines, we catch all exceptions it may produce and
  // create our own one. To this end, in the <code>catch</code>
  // clause, we let the program run into an <code>AssertThrow(false, ...)</code>
  // statement. Since the condition is always false, this always triggers an
  // exception. In other words, this is equivalent to writing
  // <code>throw ExcMessage("...")</code> but it also fills certain fields
  // in the exception object that will later be printed on the screen
  // identifying the function, file and line where the exception happened.
  std::vector<double> AfricaTopography::get_data()
  {
    std::vector<double> data;

    // create a stream where we read from gzipped data
    boost::iostreams::filtering_istream in;
    in.push(boost::iostreams::basic_gzip_decompressor<>());
    in.push(boost::iostreams::file_source("topography.txt.gz"));

    for (unsigned int line = 0; line < 83600; ++line)
      {
        try
          {
            double lat, lon, elevation;
            in >> lat >> lon >> elevation;

            data.push_back(elevation);
          }
        catch (...)
          {
            AssertThrow(false,
                        ExcMessage("Could not read all 83,600 data points "
                                   "from the file <topography.txt.gz>!"));
          }
      }

    return data;
  }


  // @sect3{Describing the geometry: AfricaGeometry}
  //
  // The following class is then the main one of this program. Its structure
  // has been described in much detail in the introduction and does not need
  // much introduction any more.
  class AfricaGeometry : public ChartManifold<3, 3>
  {
  public:
    virtual Point<3> pull_back(const Point<3> &space_point) const override;

    virtual Point<3> push_forward(const Point<3> &chart_point) const override;

    virtual std::unique_ptr<Manifold<3, 3>> clone() const override;

  private:
    static const double R;
    static const double ellipticity;

    const AfricaTopography topography;

    Point<3> push_forward_wgs84(const Point<3> &phi_theta_d) const;
    Point<3> pull_back_wgs84(const Point<3> &x) const;

    Point<3> push_forward_topo(const Point<3> &phi_theta_d_hat) const;
    Point<3> pull_back_topo(const Point<3> &phi_theta_d) const;
  };


  const double AfricaGeometry::R           = 6378137;
  const double AfricaGeometry::ellipticity = 8.1819190842622e-2;


  // The implementation, as well, is pretty straightforward if you have
  // read the introduction. In particular, both of the pull back and
  // push forward functions are just concatenations of the respective
  // functions of the WGS 84 and topography mappings:
  Point<3> AfricaGeometry::pull_back(const Point<3> &space_point) const
  {
    return pull_back_topo(pull_back_wgs84(space_point));
  }

  Point<3> AfricaGeometry::push_forward(const Point<3> &chart_point) const
  {
    return push_forward_wgs84(push_forward_topo(chart_point));
  }


  // The next function is required by the interface of the
  // Manifold base class, and allows cloning the AfricaGeometry
  // class. Notice that, while the function returns a
  // `std::unique_ptr<Manifold<3,3>>`, we internally create a
  // `unique_ptr<AfricaGeometry>`. In other words, the library
  // requires a pointer-to-base-class, which we provide by creating a
  // pointer-to-derived-class.
  std::unique_ptr<Manifold<3, 3>> AfricaGeometry::clone() const
  {
    return std::make_unique<AfricaGeometry>();
  }


  // The following two functions then define the forward and inverse
  // transformations that correspond to the WGS 84 reference shape of
  // Earth. The forward transform follows the formula shown in the
  // introduction. The inverse transform is significantly more complicated
  // and is, at the very least, not intuitive. It also suffers from the
  // fact that it returns an angle that at the end of the function we
  // need to clip back into the interval $[0,2\pi]$ if it should have
  // escaped from there.
  Point<3> AfricaGeometry::push_forward_wgs84(const Point<3> &phi_theta_d) const
  {
    const double phi   = phi_theta_d[0];
    const double theta = phi_theta_d[1];
    const double d     = phi_theta_d[2];

    const double R_bar = R / std::sqrt(1 - (ellipticity * ellipticity *
                                            std::sin(theta) * std::sin(theta)));

    return {(R_bar + d) * std::cos(phi) * std::cos(theta),
            (R_bar + d) * std::sin(phi) * std::cos(theta),
            ((1 - ellipticity * ellipticity) * R_bar + d) * std::sin(theta)};
  }

  Point<3> AfricaGeometry::pull_back_wgs84(const Point<3> &x) const
  {
    const double b   = std::sqrt(R * R * (1 - ellipticity * ellipticity));
    const double ep  = std::sqrt((R * R - b * b) / (b * b));
    const double p   = std::sqrt(x(0) * x(0) + x(1) * x(1));
    const double th  = std::atan2(R * x(2), b * p);
    const double phi = std::atan2(x(1), x(0));
    const double theta =
      std::atan2(x(2) + ep * ep * b * std::pow(std::sin(th), 3),
                 (p -
                  (ellipticity * ellipticity * R * std::pow(std::cos(th), 3))));
    const double R_bar =
      R / (std::sqrt(1 - ellipticity * ellipticity * std::sin(theta) *
                           std::sin(theta)));
    const double R_plus_d = p / std::cos(theta);

    Point<3> phi_theta_d;
    if (phi < 0)
      phi_theta_d[0] = phi + 2 * numbers::PI;
    else if (phi > 2 * numbers::PI)
      phi_theta_d[0] = phi - 2 * numbers::PI;
    else
      phi_theta_d[0] = phi;
    phi_theta_d[1] = theta;
    phi_theta_d[2] = R_plus_d - R_bar;
    return phi_theta_d;
  }


  // In contrast, the topography transformations follow exactly the
  // description in the introduction. There is not consequently not
  // much to add:
  Point<3>
  AfricaGeometry::push_forward_topo(const Point<3> &phi_theta_d_hat) const
  {
    const double d_hat = phi_theta_d_hat[2];
    const double h = topography.value(phi_theta_d_hat[0], phi_theta_d_hat[1]);
    const double d = d_hat + (d_hat + 500000) / 500000 * h;
    return {phi_theta_d_hat[0], phi_theta_d_hat[1], d};
  }

  Point<3> AfricaGeometry::pull_back_topo(const Point<3> &phi_theta_d) const
  {
    const double d     = phi_theta_d[2];
    const double h     = topography.value(phi_theta_d[0], phi_theta_d[1]);
    const double d_hat = 500000 * (d - h) / (500000 + h);
    return {phi_theta_d[0], phi_theta_d[1], d_hat};
  }


  // @sect3{Creating the mesh}
  //
  // Having so described the properties of the geometry, not it is
  // time to deal with the mesh used to discretize it. To this end,
  // we create objects for the geometry and triangulation, and then
  // proceed to create a $1\times 2\times 1$ rectangular mesh that
  // corresponds to the reference domain
  // $\hat U=[26,35]\times[-10,5]\times[-500000,0]$. We choose
  // this number of subdivisions because it leads to cells that
  // are roughly like cubes instead of stretched in one direction or
  // another.
  //
  // Of course, we are not actually interested in meshing the
  // reference domain. We are interested in meshing the real domain.
  // Consequently, we will use the GridTools::transform() function
  // that simply moves every point of a triangulation according to
  // a given transformation. The transformation function it wants is
  // a function that takes as its single argument a point in the reference
  // domain and returns the corresponding location in the domain that we
  // want to map to. This is, of course, exactly the push forward
  // function of the geometry we use. We wrap it by a lambda function to
  // obtain the kind of function object required for the transformation.
  void run()
  {
    AfricaGeometry   geometry;
    Triangulation<3> triangulation;

    {
      const Point<3> corner_points[2] = {
        Point<3>(26 * numbers::PI / 180, -10 * numbers::PI / 180, -500000),
        Point<3>(35 * numbers::PI / 180, 5 * numbers::PI / 180, 0)};
      std::vector<unsigned int> subdivisions(3);
      subdivisions[0] = 1;
      subdivisions[1] = 2;
      subdivisions[2] = 1;
      GridGenerator::subdivided_hyper_rectangle(
        triangulation, subdivisions, corner_points[0], corner_points[1], true);

      GridTools::transform(
        [&geometry](const Point<3> &chart_point) {
          return geometry.push_forward(chart_point);
        },
        triangulation);
    }

    // The next step is to explain to the triangulation to use our geometry
    // object whenever a new point is needed upon refining the mesh. We do
    // this by telling the triangulation to use our geometry for everything
    // that has manifold indicator zero, and then proceed to mark all cells
    // and their bounding faces and edges with manifold indicator zero. This
    // ensures that the triangulation consults our geometry object every time
    // a new vertex is needed. Since manifold indicators are inherited from
    // mother to children, this also happens after several recursive
    // refinement steps.
    triangulation.set_manifold(0, geometry);
    for (const auto &cell : triangulation.active_cell_iterators())
      cell->set_all_manifold_ids(0);

    // The last step is to refine the mesh beyond its initial $1\times 2\times
    // 1$ coarse mesh. We could just refine globally a number of times, but
    // since for the purpose of this tutorial program we're really only
    // interested in what is happening close to the surface, we just refine 6
    // times all of the cells that have a face at a boundary with indicator 5.
    // Looking this up in the documentation of the
    // GridGenerator::subdivided_hyper_rectangle() function we have used above
    // reveals that boundary indicator 5 corresponds to the top surface of the
    // domain (and this is what the last <code>true</code> argument in the call
    // to GridGenerator::subdivided_hyper_rectangle() above meant: to "color"
    // the boundaries by assigning each boundary a unique boundary indicator).
    for (unsigned int i = 0; i < 6; ++i)
      {
        for (const auto &cell : triangulation.active_cell_iterators())
          for (const auto &face : cell->face_iterators())
            if (face->boundary_id() == 5)
              {
                cell->set_refine_flag();
                break;
              }
        triangulation.execute_coarsening_and_refinement();

        std::cout << "Refinement step " << i + 1 << ": "
                  << triangulation.n_active_cells() << " cells, "
                  << GridTools::minimal_cell_diameter(triangulation) / 1000
                  << "km minimal cell diameter" << std::endl;
      }

    // Having done this all, we can now output the mesh into a file of its own:
    const std::string filename = "mesh.vtu";
    std::ofstream     out(filename);
    GridOut           grid_out;
    grid_out.write_vtu(triangulation, out);
  }
} // namespace Step53



// @sect3{The main function}

// Finally, the main function, which follows the same scheme used in all
// tutorial programs starting with step-6. There isn't much to do here, only
// to call the single <code>run()</code> function.
int main()
{
  try
    {
      Step53::run();
    }
  catch (std::exception &exc)
    {
      std::cerr << std::endl
                << std::endl
                << "----------------------------------------------------"
                << std::endl;
      std::cerr << "Exception on processing: " << std::endl
                << exc.what() << std::endl
                << "Aborting!" << std::endl
                << "----------------------------------------------------"
                << std::endl;

      return 1;
    }
  catch (...)
    {
      std::cerr << std::endl
                << std::endl
                << "----------------------------------------------------"
                << std::endl;
      std::cerr << "Unknown exception!" << std::endl
                << "Aborting!" << std::endl
                << "----------------------------------------------------"
                << std::endl;
      return 1;
    }
}
